Sir, One more question. How can I know the space group of the supercell? I searched but was unable to find it. Thank you!
On Sat, Jul 25, 2020 at 6:20 AM Peeyush Kumar Kamlesh < [email protected]> wrote: > Thank you So much Prof. Blaha. It is working now. > > > > On Fri, Jul 24, 2020 at 3:39 PM Peeyush Kumar Kamlesh < > [email protected]> wrote: > >> Sir, >> Output of x nn is: >> ----------------------------------------- >> >> specify nn-bondlength factor: (usually=2) [and optionally dlimit, dstmax >> (about >> 1.d-5, 20)] >> DSTMAX: 30.2976897600000 >> iix,iiy,iiz 2 2 2 54.5904320000000 >> 54.5904320000000 54.5904320000000 >> >> ATOM 1 Rb ATOM 41 Zn >> RMT( 1)=2.50000 AND RMT( 41)=2.50000 >> SUMS TO 5.00000 LT. NN-DIST= 5.89806 >> >> And so on till >> >> ATOM 96 Bi ATOM 40 Zn >> RMT( 96)=2.50000 AND RMT( 40)=2.50000 >> SUMS TO 5.00000 LT. NN-DIST= 5.90959 >> WARNING: Mult not equal. PLEASE CHECK outputnn-file >> WARNING: Mult not equal. PLEASE CHECK outputnn-file >> >> -------------------------------------------- >> >> When I ignore this warning and accept the changes produced by nn, then it >> pops up a new question (Use new struct-file?). on clicking on YES, it >> Displays a message: >> >> >> *Case-001.struct_nn copied to case-001.struct old struct-file saved as >> case-001.struct_init case-001.inst updated* >> And ask to start StructGen again. >> On ignoring this question, when I click on x sgroup, it shows following >> warning: >> >> *warning: !!! Number of inequivalent atoms has changed. !!! Old value= 34 >> New value= 40 warning: !!! Bravais lattice has changed. sgroup found: 35 (C >> m m 2) Note that shift vectors for this space group are defined.* >> On further proceeding, it reflects an error in dstart;- >> >> *ROTDEF - Error >> 0.0u 0.0s 0:00.68 4.4% 0+0k 29488+24io 82pf+0w* >> >> On the contrary, if I agree on start StructGen again, and run x sgroup >> then it again show the following warning: >> >> *warning: !!! Number of inequivalent atoms has changed. !!! Old value= 96 >> New value= 40 warning: !!! Bravais lattice has changed. sgroup found: 35 (C >> m m 2) Note that shift vectors for this space group are defined.* >> *warning: !!! Bravais lattice has changed.* >> And ask to accept a new file generated by sgroup. When I accept it then >> in further process, it does not show any error. >> >> But in the Phonopy manual it has been written that, *"Calculate forces >> on atoms in the supercells with displacements. It is necessary to use >> case.struct_nn file when running init_lapw. Note that case.struct_sgroup >> file can’t be used with phonopy."* >> >> *I am confused, how should I proceed further?* >> >> Thank you! >> >> >> On Fri, Jul 24, 2020 at 11:56 AM Peeyush Kumar Kamlesh < >> [email protected]> wrote: >> >>> Dear Blaha Sir, >>> 1. First I prepared a case.struct file with optimized lattice >>> parameters, having F43m spacegroup (216). Which F lattice. it is as follows: >>> ---------------------------------------------------------- >>> >>> F LATTICE,NONEQUIV.ATOMS: 3 216_F-43m >>> MODE OF CALC=RELA unit=ang >>> 13.647608 13.647608 13.647608 90.000000 90.000000 90.000000 >>> ATOM 1: X=0.50000000 Y=0.50000000 Z=0.50000000 >>> MULT= 1 ISPLIT= 2 >>> Rb NPT= 781 R0=0.00001000 RMT= 2.5000 Z: 37.000 >>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 >>> 0.0000000 1.0000000 0.0000000 >>> 0.0000000 0.0000000 1.0000000 >>> ATOM 2: X=0.25000000 Y=0.25000000 Z=0.25000000 >>> MULT= 1 ISPLIT= 2 >>> Zn NPT= 781 R0=0.00005000 RMT= 2.5000 Z: 30.000 >>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 >>> 0.0000000 1.0000000 0.0000000 >>> 0.0000000 0.0000000 1.0000000 >>> ATOM 3: X=0.00000000 Y=0.00000000 Z=0.00000000 >>> MULT= 1 ISPLIT= 2 >>> Bi NPT= 781 R0=0.00000500 RMT= 2.5000 Z: 83.000 >>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 >>> 0.0000000 1.0000000 0.0000000 >>> 0.0000000 0.0000000 1.0000000 >>> 24 NUMBER OF SYMMETRY OPERATIONS >>> >>> ------------------------------------------------------------------------------------ >>> 2. Then I created a supercell (1x1x1) using wien2k, having P lattice but >>> with the same space group. case_super .struct file is as follows: >>> ----------------------------------------------------------- >>> >>> P LATTICE,NONEQUIV. ATOMS 12 >>> MODE OF CALC=RELA unit=ang >>> 13.647608 13.647608 13.647608 90.000000 90.000000 90.000000 >>> ATOM 1: X=0.50000000 Y=0.50000000 Z=0.50000000 >>> MULT= 1 ISPLIT= 2 >>> Rb NPT= 781 R0=0.00001000 RMT= 2.5000 Z: 37.0 >>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 >>> 0.0000000 1.0000000 0.0000000 >>> 0.0000000 0.0000000 1.0000000 >>> And so on ................. till >>> ATOM 12: X=0.00000000 Y=0.50000000 Z=0.50000000 >>> MULT= 1 ISPLIT= 2 >>> Bi NPT= 781 R0=0.00000500 RMT= 2.5000 Z: 83.0 >>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 >>> 0.0000000 1.0000000 0.0000000 >>> 0.0000000 0.0000000 1.0000000 >>> 0 NUMBER OF SYMMETRY OPERATIONS >>> ------------------------------------------------------------- >>> 3. Then I copied case_super.struct to case.struct file and used the >>> command (phonopy --wien2k -d --dim="2 2 2" -c case.struct) to run phonopy >>> with a supercell of (2x2x2). its output is as follows: >>> --------------------------------------------------- >>> _ >>> _ __ | |__ ___ _ __ ___ _ __ _ _ >>> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | >>> | |_) | | | | (_) | | | | (_) || |_) | |_| | >>> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | >>> |_| |_| |___/ >>> 2.7.0 >>> >>> Python version 3.8.4 >>> Spglib version 1.15.1 >>> >>> Calculator interface: wien2k >>> Crystal structure was read from "RbZnBi.struct". >>> Unit of length: au >>> Displacements creation mode >>> Settings: >>> Supercell: [2 2 2] >>> Spacegroup: F-43m (216) >>> Use -v option to watch primitive cell, unit cell, and supercell >>> structures. >>> >>> Number of non-equivalent atoms in RbZnBi.structS-001.in: 40 >>> Number of non-equivalent atoms in RbZnBi.structS-002.in: 38 >>> Number of non-equivalent atoms in RbZnBi.structS-003.in: 40 >>> "phonopy_disp.yaml" and supercells have been created. >>> >>> Summary of calculation was written in "phonopy_disp.yaml". >>> _ >>> ___ _ __ __| | >>> / _ \ '_ \ / _` | >>> | __/ | | | (_| | >>> \___|_| |_|\__,_| >>> ------------------------------------------------------------------------ >>> >>> 4. It is clear from the output that the space group is not changed. It >>> generates one file for a perfect supercell and 3 files (case-xxx.struct) >>> for supercells with displacements. case-xxx.struct is as follows: >>> --------------------------------------------------- >>> Title >>> P LATTICE,NONEQUIV.ATOMS: 96 >>> MODE OF CALC=RELA >>> 27.295216 27.295216 27.295216 90.000000 90.000000 90.000000 >>> ATOM -1: X=0.25073273 Y=0.25000000 Z=0.25000000 >>> MULT= 1 ISPLIT= 8 >>> Rb NPT= 781 R0=0.00001000 RMT= 2.50000 Z: 37.0 >>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 >>> 0.0000000 1.0000000 0.0000000 >>> 0.0000000 0.0000000 1.0000000 >>> And so on.........till >>> ATOM -96: X=0.50000000 Y=0.75000000 Z=0.75000000 >>> MULT= 1 ISPLIT= 8 >>> Bi NPT= 781 R0=0.00000500 RMT= 3.0000 Z: 83.000 >>> LOCAL ROT MATRIX: 1.0000000 0.0000000 0.0000000 >>> 0.0000000 1.0000000 0.0000000 >>> 0.0000000 0.0000000 1.0000000 >>> 0 NUMBER OF SYMMETRY OPERATIONS >>> >>> -------------------------------------------------------------------------------------- >>> 5. Then I picked one of the case-xxx.struct files and put in another >>> directory for initialization and started step by step initialization. and >>> perform x nn: Which Shows following warning: >>> >>> WARNING: Mult not equal. PLEASE CHECK outputnn-file >>> WARNING: ityp not equal. PLEASE CHECK outputnn-file >>> >>> 6. Then I tried to increase RMT up 3. It now shows the following message: >>> ERROR !!!!!!!!!!!!!!! >>> RMT( 1)=3.00000 AND RMT( 41)=3.00000 >>> SUMS TO 6.00000 GT NNN-DIST= 5.89806 >>> WARNING: Mult not equal. PLEASE CHECK outputnn-file >>> WARNING: ityp not equal. PLEASE CHECK outputnn-file >>> >>> Please suggest What should I do? I shall be grateful to you! >>> >>> Thanks and Regards >>> >>> >>> On Fri, Jul 24, 2020 at 1:53 AM Peeyush Kumar Kamlesh < >>> [email protected]> wrote: >>> >>>> Before that when I run the command x nn, it shows following error: >>>> >>>> WARNING: Mult not equal. PLEASE CHECK outputnn-file >>>> WARNING: ityp not equal. PLEASE CHECK outputnn-file >>>> >>>> I have tried by putting different values for nn, but it is not changing. >>>> >>>> What will be its solution? >>>> >>>> >>>> On Fri, Jul 24, 2020 at 1:33 AM Peeyush Kumar Kamlesh < >>>> [email protected]> wrote: >>>> >>>>> Dear Wien2k users, >>>>> Greetings! >>>>> I am working on XYZ half-Heusler compounds with space group no.-216. >>>>> When I do initialization of a struct file of a supercell. then output of >>>>> x >>>>> sgroup shows some warning: >>>>> >>>>> warning: !!! Number of inequivalent atoms has changed. !!! Old value= >>>>> 34 New value= 40 warning: !!! Bravais lattice has changed. >>>>> sgroup found: 35 (C m m 2) Note that shift vectors for this space >>>>> group are defined. >>>>> Bravais lattice: Orthorhombic C-base centred. >>>>> Kindly help me to solve the problem. >>>>> >>>>> Thank you! >>>>> >>>>
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